rs2256038

Variant names:

• chr21-15148855-G-A
• rs2256038
• ENST00000798068.1:n.161-5733G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000798068.1(ENSG00000303916):​n.161-5733G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,032 control chromosomes in the GnomAD database, including 22,008 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (22008 hom., cov: 32)
• Consequence: ENSG00000303916 ENST00000798068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 3 publications found

Genes affected

ENSG00000303916 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798068.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303916	ENST00000798068.1		n.161-5733G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75370 AN: 151914 Hom.: 21921 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.467

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.497 AC: 75533 AN: 152032 Hom.: 22008 Cov.: 32 AF XY: 0.499 AC XY: 37123 AN XY: 74330

African (AFR) AF: 0.817 AC: 33904 AN: 41490

American (AMR) AF: 0.471 AC: 7194 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1225 AN: 3468

East Asian (EAS) AF: 0.493 AC: 2541 AN: 5158

South Asian (SAS) AF: 0.411 AC: 1980 AN: 4822

European-Finnish (FIN) AF: 0.380 AC: 4005 AN: 10550

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23199 AN: 67956

Other (OTH) AF: 0.475 AC: 1003 AN: 2112

Alfa AF: 0.391 Hom.: 16694

Bravo AF: 0.519

Asia WGS AF: 0.518 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.42
DANN	Benign	0.48
PhyloP100		-0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2256038;

hg19: chr21-16521176;